Starting phenix.real_space_refine on Sun Dec 29 15:18:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cd9_45464/12_2024/9cd9_45464.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cd9_45464/12_2024/9cd9_45464.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cd9_45464/12_2024/9cd9_45464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cd9_45464/12_2024/9cd9_45464.map" model { file = "/net/cci-nas-00/data/ceres_data/9cd9_45464/12_2024/9cd9_45464.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cd9_45464/12_2024/9cd9_45464.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 6853 2.51 5 N 1914 2.21 5 O 2222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10989 Number of models: 1 Model: "" Number of chains: 2 Chain: "E" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 549 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain: "F" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 450 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Restraints were copied for chains: H, J, L, N, P, R, T, V, X, Z, G, I, K, M, O, Q, S, U, W, Y Time building chain proxies: 3.11, per 1000 atoms: 0.28 Number of scatterers: 10989 At special positions: 0 Unit cell: (113.424, 92.574, 70.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2222 8.00 N 1914 7.00 C 6853 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 1.3 seconds 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2706 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 50.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'I' and resid 16 through 20 removed outlier: 6.486A pdb=" N VAL E 16 " --> pdb=" O ALA G 17 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N ALA G 19 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA E 18 " --> pdb=" O ALA G 19 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL G 16 " --> pdb=" O ALA S 17 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ALA S 19 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA G 18 " --> pdb=" O ALA S 19 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL U 16 " --> pdb=" O ALA W 17 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N ALA W 19 " --> pdb=" O VAL U 16 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA U 18 " --> pdb=" O ALA W 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 25 through 30 removed outlier: 6.520A pdb=" N VAL E 26 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ALA G 29 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU E 28 " --> pdb=" O ALA G 29 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL G 26 " --> pdb=" O ALA S 27 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ALA S 29 " --> pdb=" O VAL G 26 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLU G 28 " --> pdb=" O ALA S 29 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL U 26 " --> pdb=" O ALA W 27 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ALA W 29 " --> pdb=" O VAL U 26 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU U 28 " --> pdb=" O ALA W 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 38 through 40 removed outlier: 6.265A pdb=" N LEU E 38 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU G 38 " --> pdb=" O TYR S 39 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU U 38 " --> pdb=" O TYR W 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 43 through 50 removed outlier: 8.794A pdb=" N LYS E 43 " --> pdb=" O THR I 44 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N GLU I 46 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N LYS E 45 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N VAL I 48 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY E 47 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N HIS I 50 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL E 49 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR E 44 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS G 45 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLU E 46 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLY G 47 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR G 44 " --> pdb=" O LYS S 43 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS S 45 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLU G 46 " --> pdb=" O LYS S 45 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY S 47 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N LYS Q 43 " --> pdb=" O THR S 44 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N GLU S 46 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N LYS Q 45 " --> pdb=" O GLU S 46 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N VAL S 48 " --> pdb=" O LYS Q 45 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLY Q 47 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N HIS S 50 " --> pdb=" O GLY Q 47 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL Q 49 " --> pdb=" O HIS S 50 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N LYS O 43 " --> pdb=" O THR Q 44 " (cutoff:3.500A) removed outlier: 10.221A pdb=" N GLU Q 46 " --> pdb=" O LYS O 43 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N LYS O 45 " --> pdb=" O GLU Q 46 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N VAL Q 48 " --> pdb=" O LYS O 45 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY O 47 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N HIS Q 50 " --> pdb=" O GLY O 47 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL O 49 " --> pdb=" O HIS Q 50 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N LYS M 43 " --> pdb=" O THR O 44 " (cutoff:3.500A) removed outlier: 10.240A pdb=" N GLU O 46 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N LYS M 45 " --> pdb=" O GLU O 46 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N VAL O 48 " --> pdb=" O LYS M 45 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLY M 47 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N HIS O 50 " --> pdb=" O GLY M 47 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL M 49 " --> pdb=" O HIS O 50 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N LYS K 43 " --> pdb=" O THR M 44 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N GLU M 46 " --> pdb=" O LYS K 43 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N LYS K 45 " --> pdb=" O GLU M 46 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N VAL M 48 " --> pdb=" O LYS K 45 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY K 47 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N HIS M 50 " --> pdb=" O GLY K 47 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL K 49 " --> pdb=" O HIS M 50 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N LYS Y 43 " --> pdb=" O THR K 44 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N GLU K 46 " --> pdb=" O LYS Y 43 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N LYS Y 45 " --> pdb=" O GLU K 46 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N VAL K 48 " --> pdb=" O LYS Y 45 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLY Y 47 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N HIS K 50 " --> pdb=" O GLY Y 47 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL Y 49 " --> pdb=" O HIS K 50 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N LYS U 43 " --> pdb=" O THR Y 44 " (cutoff:3.500A) removed outlier: 10.221A pdb=" N GLU Y 46 " --> pdb=" O LYS U 43 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N LYS U 45 " --> pdb=" O GLU Y 46 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N VAL Y 48 " --> pdb=" O LYS U 45 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY U 47 " --> pdb=" O VAL Y 48 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N HIS Y 50 " --> pdb=" O GLY U 47 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL U 49 " --> pdb=" O HIS Y 50 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR U 44 " --> pdb=" O LYS W 43 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LYS W 45 " --> pdb=" O THR U 44 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLU U 46 " --> pdb=" O LYS W 45 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLY W 47 " --> pdb=" O GLU U 46 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 55 through 66 removed outlier: 8.967A pdb=" N VAL E 55 " --> pdb=" O ALA I 56 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N LYS I 58 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLU E 57 " --> pdb=" O LYS I 58 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N LYS I 60 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR E 59 " --> pdb=" O LYS I 60 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLN I 62 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLU E 61 " --> pdb=" O GLN I 62 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N THR I 64 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL E 63 " --> pdb=" O THR I 64 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL I 66 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASN E 65 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL G 55 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA E 56 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLU G 57 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL S 55 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA G 56 " --> pdb=" O VAL S 55 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLU S 57 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N VAL Q 55 " --> pdb=" O ALA S 56 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N LYS S 58 " --> pdb=" O VAL Q 55 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU Q 57 " --> pdb=" O LYS S 58 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N LYS S 60 " --> pdb=" O GLU Q 57 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR Q 59 " --> pdb=" O LYS S 60 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N GLN S 62 " --> pdb=" O THR Q 59 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU Q 61 " --> pdb=" O GLN S 62 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N THR S 64 " --> pdb=" O GLU Q 61 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL Q 63 " --> pdb=" O THR S 64 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL S 66 " --> pdb=" O VAL Q 63 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASN Q 65 " --> pdb=" O VAL S 66 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N VAL O 55 " --> pdb=" O ALA Q 56 " (cutoff:3.500A) removed outlier: 9.964A pdb=" N LYS Q 58 " --> pdb=" O VAL O 55 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLU O 57 " --> pdb=" O LYS Q 58 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N LYS Q 60 " --> pdb=" O GLU O 57 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR O 59 " --> pdb=" O LYS Q 60 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLN Q 62 " --> pdb=" O THR O 59 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLU O 61 " --> pdb=" O GLN Q 62 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N THR Q 64 " --> pdb=" O GLU O 61 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL O 63 " --> pdb=" O THR Q 64 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL Q 66 " --> pdb=" O VAL O 63 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASN O 65 " --> pdb=" O VAL Q 66 " (cutoff:3.500A) removed outlier: 8.974A pdb=" N VAL M 55 " --> pdb=" O ALA O 56 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N LYS O 58 " --> pdb=" O VAL M 55 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU M 57 " --> pdb=" O LYS O 58 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N LYS O 60 " --> pdb=" O GLU M 57 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR M 59 " --> pdb=" O LYS O 60 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N GLN O 62 " --> pdb=" O THR M 59 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLU M 61 " --> pdb=" O GLN O 62 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N THR O 64 " --> pdb=" O GLU M 61 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL M 63 " --> pdb=" O THR O 64 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL O 66 " --> pdb=" O VAL M 63 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASN M 65 " --> pdb=" O VAL O 66 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N VAL K 55 " --> pdb=" O ALA M 56 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N LYS M 58 " --> pdb=" O VAL K 55 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLU K 57 " --> pdb=" O LYS M 58 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N LYS M 60 " --> pdb=" O GLU K 57 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR K 59 " --> pdb=" O LYS M 60 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLN M 62 " --> pdb=" O THR K 59 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLU K 61 " --> pdb=" O GLN M 62 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N THR M 64 " --> pdb=" O GLU K 61 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL K 63 " --> pdb=" O THR M 64 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL M 66 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASN K 65 " --> pdb=" O VAL M 66 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N VAL Y 55 " --> pdb=" O ALA K 56 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N LYS K 58 " --> pdb=" O VAL Y 55 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU Y 57 " --> pdb=" O LYS K 58 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N LYS K 60 " --> pdb=" O GLU Y 57 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR Y 59 " --> pdb=" O LYS K 60 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N GLN K 62 " --> pdb=" O THR Y 59 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLU Y 61 " --> pdb=" O GLN K 62 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N THR K 64 " --> pdb=" O GLU Y 61 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL Y 63 " --> pdb=" O THR K 64 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL K 66 " --> pdb=" O VAL Y 63 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASN Y 65 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N VAL U 55 " --> pdb=" O ALA Y 56 " (cutoff:3.500A) removed outlier: 9.964A pdb=" N LYS Y 58 " --> pdb=" O VAL U 55 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLU U 57 " --> pdb=" O LYS Y 58 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N LYS Y 60 " --> pdb=" O GLU U 57 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR U 59 " --> pdb=" O LYS Y 60 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N GLN Y 62 " --> pdb=" O THR U 59 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLU U 61 " --> pdb=" O GLN Y 62 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N THR Y 64 " --> pdb=" O GLU U 61 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL U 63 " --> pdb=" O THR Y 64 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL Y 66 " --> pdb=" O VAL U 63 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN U 65 " --> pdb=" O VAL Y 66 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL W 55 " --> pdb=" O THR U 54 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA U 56 " --> pdb=" O VAL W 55 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU W 57 " --> pdb=" O ALA U 56 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 69 through 71 removed outlier: 6.416A pdb=" N VAL E 70 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL Q 70 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL O 70 " --> pdb=" O VAL Q 71 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL M 70 " --> pdb=" O VAL O 71 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL K 70 " --> pdb=" O VAL M 71 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL Y 70 " --> pdb=" O VAL K 71 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL U 70 " --> pdb=" O VAL Y 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 75 through 80 removed outlier: 6.677A pdb=" N THR G 75 " --> pdb=" O ALA S 76 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ALA S 78 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL G 77 " --> pdb=" O ALA S 78 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LYS S 80 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLN G 79 " --> pdb=" O LYS S 80 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA Q 76 " --> pdb=" O VAL S 77 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLN S 79 " --> pdb=" O ALA Q 76 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ALA Q 78 " --> pdb=" O GLN S 79 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA M 76 " --> pdb=" O VAL O 77 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLN O 79 " --> pdb=" O ALA M 76 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ALA M 78 " --> pdb=" O GLN O 79 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA Y 76 " --> pdb=" O VAL K 77 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLN K 79 " --> pdb=" O ALA Y 76 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ALA Y 78 " --> pdb=" O GLN K 79 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 89 through 93 removed outlier: 6.387A pdb=" N ALA E 89 " --> pdb=" O ALA G 90 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N THR G 92 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ALA E 91 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA G 89 " --> pdb=" O ALA S 90 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N THR S 92 " --> pdb=" O ALA G 89 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ALA G 91 " --> pdb=" O THR S 92 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA U 89 " --> pdb=" O ALA W 90 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N THR W 92 " --> pdb=" O ALA U 89 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ALA U 91 " --> pdb=" O THR W 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 38 through 40 removed outlier: 6.381A pdb=" N TYR F 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR R 39 " --> pdb=" O VAL T 40 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR P 39 " --> pdb=" O VAL R 40 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR N 39 " --> pdb=" O VAL P 40 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N TYR L 39 " --> pdb=" O VAL N 40 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR Z 39 " --> pdb=" O VAL L 40 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N TYR V 39 " --> pdb=" O VAL Z 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 45 through 57 removed outlier: 9.031A pdb=" N LYS F 45 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N VAL J 48 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLY F 47 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N HIS J 50 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL F 49 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL J 52 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N GLY F 51 " --> pdb=" O VAL J 52 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N THR J 54 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ALA F 53 " --> pdb=" O THR J 54 " (cutoff:3.500A) removed outlier: 10.436A pdb=" N ALA J 56 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N VAL F 55 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLU F 46 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY H 47 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL F 52 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA H 53 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR F 54 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL H 55 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA F 56 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLU H 57 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLU H 46 " --> pdb=" O LYS T 45 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLY T 47 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL H 52 " --> pdb=" O GLY T 51 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA T 53 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR H 54 " --> pdb=" O ALA T 53 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL T 55 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA H 56 " --> pdb=" O VAL T 55 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLU T 57 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N LYS R 45 " --> pdb=" O GLU T 46 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N VAL T 48 " --> pdb=" O LYS R 45 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLY R 47 " --> pdb=" O VAL T 48 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N HIS T 50 " --> pdb=" O GLY R 47 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL R 49 " --> pdb=" O HIS T 50 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL T 52 " --> pdb=" O VAL R 49 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLY R 51 " --> pdb=" O VAL T 52 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N THR T 54 " --> pdb=" O GLY R 51 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ALA R 53 " --> pdb=" O THR T 54 " (cutoff:3.500A) removed outlier: 10.425A pdb=" N ALA T 56 " --> pdb=" O ALA R 53 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N VAL R 55 " --> pdb=" O ALA T 56 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N LYS P 45 " --> pdb=" O GLU R 46 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N VAL R 48 " --> pdb=" O LYS P 45 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY P 47 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N HIS R 50 " --> pdb=" O GLY P 47 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL P 49 " --> pdb=" O HIS R 50 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL R 52 " --> pdb=" O VAL P 49 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N GLY P 51 " --> pdb=" O VAL R 52 " (cutoff:3.500A) removed outlier: 9.734A pdb=" N THR R 54 " --> pdb=" O GLY P 51 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N ALA P 53 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 10.436A pdb=" N ALA R 56 " --> pdb=" O ALA P 53 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N VAL P 55 " --> pdb=" O ALA R 56 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N LYS N 45 " --> pdb=" O GLU P 46 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N VAL P 48 " --> pdb=" O LYS N 45 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY N 47 " --> pdb=" O VAL P 48 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N HIS P 50 " --> pdb=" O GLY N 47 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL N 49 " --> pdb=" O HIS P 50 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL P 52 " --> pdb=" O VAL N 49 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLY N 51 " --> pdb=" O VAL P 52 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N THR P 54 " --> pdb=" O GLY N 51 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ALA N 53 " --> pdb=" O THR P 54 " (cutoff:3.500A) removed outlier: 10.427A pdb=" N ALA P 56 " --> pdb=" O ALA N 53 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N VAL N 55 " --> pdb=" O ALA P 56 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N LYS L 45 " --> pdb=" O GLU N 46 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N VAL N 48 " --> pdb=" O LYS L 45 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLY L 47 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N HIS N 50 " --> pdb=" O GLY L 47 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL L 49 " --> pdb=" O HIS N 50 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL N 52 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N GLY L 51 " --> pdb=" O VAL N 52 " (cutoff:3.500A) removed outlier: 9.732A pdb=" N THR N 54 " --> pdb=" O GLY L 51 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ALA L 53 " --> pdb=" O THR N 54 " (cutoff:3.500A) removed outlier: 10.436A pdb=" N ALA N 56 " --> pdb=" O ALA L 53 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N VAL L 55 " --> pdb=" O ALA N 56 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N LYS Z 45 " --> pdb=" O GLU L 46 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N VAL L 48 " --> pdb=" O LYS Z 45 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLY Z 47 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N HIS L 50 " --> pdb=" O GLY Z 47 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL Z 49 " --> pdb=" O HIS L 50 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL L 52 " --> pdb=" O VAL Z 49 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLY Z 51 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 9.720A pdb=" N THR L 54 " --> pdb=" O GLY Z 51 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ALA Z 53 " --> pdb=" O THR L 54 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N ALA L 56 " --> pdb=" O ALA Z 53 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N VAL Z 55 " --> pdb=" O ALA L 56 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N LYS V 45 " --> pdb=" O GLU Z 46 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N VAL Z 48 " --> pdb=" O LYS V 45 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLY V 47 " --> pdb=" O VAL Z 48 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N HIS Z 50 " --> pdb=" O GLY V 47 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL V 49 " --> pdb=" O HIS Z 50 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL Z 52 " --> pdb=" O VAL V 49 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N GLY V 51 " --> pdb=" O VAL Z 52 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N THR Z 54 " --> pdb=" O GLY V 51 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ALA V 53 " --> pdb=" O THR Z 54 " (cutoff:3.500A) removed outlier: 10.435A pdb=" N ALA Z 56 " --> pdb=" O ALA V 53 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N VAL V 55 " --> pdb=" O ALA Z 56 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLU V 46 " --> pdb=" O LYS X 45 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY X 47 " --> pdb=" O GLU V 46 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL V 52 " --> pdb=" O GLY X 51 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA X 53 " --> pdb=" O VAL V 52 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR V 54 " --> pdb=" O ALA X 53 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL X 55 " --> pdb=" O THR V 54 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA V 56 " --> pdb=" O VAL X 55 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLU X 57 " --> pdb=" O ALA V 56 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 62 through 66 removed outlier: 6.360A pdb=" N GLN F 62 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ASN H 65 " --> pdb=" O GLN F 62 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR F 64 " --> pdb=" O ASN H 65 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLN H 62 " --> pdb=" O VAL T 63 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASN T 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR H 64 " --> pdb=" O ASN T 65 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLN V 62 " --> pdb=" O VAL X 63 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ASN X 65 " --> pdb=" O GLN V 62 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR V 64 " --> pdb=" O ASN X 65 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 69 through 71 removed outlier: 6.542A pdb=" N VAL F 70 " --> pdb=" O VAL J 71 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA F 69 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA H 69 " --> pdb=" O VAL T 70 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL L 70 " --> pdb=" O VAL N 71 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA V 69 " --> pdb=" O VAL X 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 75 through 83 removed outlier: 6.860A pdb=" N THR J 81 " --> pdb=" O LYS F 80 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL F 82 " --> pdb=" O THR J 81 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLU J 83 " --> pdb=" O VAL F 82 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR F 75 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ALA H 78 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL F 77 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N LYS H 80 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N GLN F 79 " --> pdb=" O LYS H 80 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL H 82 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N THR F 81 " --> pdb=" O VAL H 82 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR H 75 " --> pdb=" O ALA T 76 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ALA T 78 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL H 77 " --> pdb=" O ALA T 78 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LYS T 80 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N GLN H 79 " --> pdb=" O LYS T 80 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N VAL T 82 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N THR H 81 " --> pdb=" O VAL T 82 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR T 81 " --> pdb=" O LYS R 80 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL R 82 " --> pdb=" O THR T 81 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLU T 83 " --> pdb=" O VAL R 82 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR R 81 " --> pdb=" O LYS P 80 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL P 82 " --> pdb=" O THR R 81 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLU R 83 " --> pdb=" O VAL P 82 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR P 81 " --> pdb=" O LYS N 80 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL N 82 " --> pdb=" O THR P 81 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLU P 83 " --> pdb=" O VAL N 82 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR N 81 " --> pdb=" O LYS L 80 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL L 82 " --> pdb=" O THR N 81 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLU N 83 " --> pdb=" O VAL L 82 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR L 81 " --> pdb=" O LYS Z 80 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL Z 82 " --> pdb=" O THR L 81 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLU L 83 " --> pdb=" O VAL Z 82 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR Z 81 " --> pdb=" O LYS V 80 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL V 82 " --> pdb=" O THR Z 81 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLU Z 83 " --> pdb=" O VAL V 82 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR V 75 " --> pdb=" O ALA X 76 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ALA X 78 " --> pdb=" O THR V 75 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL V 77 " --> pdb=" O ALA X 78 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N LYS X 80 " --> pdb=" O VAL V 77 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N GLN V 79 " --> pdb=" O LYS X 80 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL X 82 " --> pdb=" O GLN V 79 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N THR V 81 " --> pdb=" O VAL X 82 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 91 through 96 removed outlier: 6.889A pdb=" N THR F 92 " --> pdb=" O ALA J 91 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY J 93 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N ALA F 91 " --> pdb=" O THR H 92 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N PHE H 94 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY F 93 " --> pdb=" O PHE H 94 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LYS H 96 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL F 95 " --> pdb=" O LYS H 96 " (cutoff:3.500A) removed outlier: 9.153A pdb=" N ALA H 91 " --> pdb=" O THR T 92 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N PHE T 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLY H 93 " --> pdb=" O PHE T 94 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N LYS T 96 " --> pdb=" O GLY H 93 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL H 95 " --> pdb=" O LYS T 96 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR R 92 " --> pdb=" O ALA T 91 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY T 93 " --> pdb=" O THR R 92 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR P 92 " --> pdb=" O ALA R 91 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY R 93 " --> pdb=" O THR P 92 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR N 92 " --> pdb=" O ALA P 91 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY P 93 " --> pdb=" O THR N 92 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR L 92 " --> pdb=" O ALA N 91 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY N 93 " --> pdb=" O THR L 92 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR Z 92 " --> pdb=" O ALA L 91 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY L 93 " --> pdb=" O THR Z 92 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR V 92 " --> pdb=" O ALA Z 91 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY Z 93 " --> pdb=" O THR V 92 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N ALA V 91 " --> pdb=" O THR X 92 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N PHE X 94 " --> pdb=" O ALA V 91 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY V 93 " --> pdb=" O PHE X 94 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LYS X 96 " --> pdb=" O GLY V 93 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL V 95 " --> pdb=" O LYS X 96 " (cutoff:3.500A) 289 hydrogen bonds defined for protein. 867 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.30 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 1958 1.28 - 1.35: 1716 1.35 - 1.41: 388 1.41 - 1.48: 1823 1.48 - 1.55: 5148 Bond restraints: 11033 Sorted by residual: bond pdb=" C GLY W 36 " pdb=" O GLY W 36 " ideal model delta sigma weight residual 1.238 1.230 0.008 8.90e-03 1.26e+04 8.26e-01 bond pdb=" C GLY E 36 " pdb=" O GLY E 36 " ideal model delta sigma weight residual 1.238 1.230 0.008 8.90e-03 1.26e+04 7.89e-01 bond pdb=" CA GLN V 99 " pdb=" CB GLN V 99 " ideal model delta sigma weight residual 1.528 1.505 0.023 2.61e-02 1.47e+03 7.78e-01 bond pdb=" CA LYS U 34 " pdb=" C LYS U 34 " ideal model delta sigma weight residual 1.526 1.516 0.010 1.08e-02 8.57e+03 7.78e-01 bond pdb=" CA LYS E 34 " pdb=" C LYS E 34 " ideal model delta sigma weight residual 1.526 1.516 0.009 1.08e-02 8.57e+03 7.73e-01 ... (remaining 11028 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.61: 12264 0.61 - 1.23: 2097 1.23 - 1.84: 362 1.84 - 2.45: 125 2.45 - 3.06: 57 Bond angle restraints: 14905 Sorted by residual: angle pdb=" N THR V 64 " pdb=" CA THR V 64 " pdb=" C THR V 64 " ideal model delta sigma weight residual 108.90 105.87 3.03 1.63e+00 3.76e-01 3.45e+00 angle pdb=" N THR T 64 " pdb=" CA THR T 64 " pdb=" C THR T 64 " ideal model delta sigma weight residual 108.90 105.87 3.03 1.63e+00 3.76e-01 3.45e+00 angle pdb=" N THR R 64 " pdb=" CA THR R 64 " pdb=" C THR R 64 " ideal model delta sigma weight residual 108.90 105.88 3.02 1.63e+00 3.76e-01 3.44e+00 angle pdb=" N THR Z 64 " pdb=" CA THR Z 64 " pdb=" C THR Z 64 " ideal model delta sigma weight residual 108.90 105.89 3.01 1.63e+00 3.76e-01 3.42e+00 angle pdb=" N THR X 64 " pdb=" CA THR X 64 " pdb=" C THR X 64 " ideal model delta sigma weight residual 108.90 105.89 3.01 1.63e+00 3.76e-01 3.41e+00 ... (remaining 14900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.45: 5484 13.45 - 26.90: 610 26.90 - 40.35: 264 40.35 - 53.80: 55 53.80 - 67.25: 44 Dihedral angle restraints: 6457 sinusoidal: 2145 harmonic: 4312 Sorted by residual: dihedral pdb=" CB LYS E 23 " pdb=" CG LYS E 23 " pdb=" CD LYS E 23 " pdb=" CE LYS E 23 " ideal model delta sinusoidal sigma weight residual 180.00 121.05 58.95 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB LYS I 23 " pdb=" CG LYS I 23 " pdb=" CD LYS I 23 " pdb=" CE LYS I 23 " ideal model delta sinusoidal sigma weight residual 180.00 121.08 58.92 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB LYS Q 23 " pdb=" CG LYS Q 23 " pdb=" CD LYS Q 23 " pdb=" CE LYS Q 23 " ideal model delta sinusoidal sigma weight residual 180.00 121.10 58.90 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 6454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 735 0.026 - 0.051: 625 0.051 - 0.076: 257 0.076 - 0.102: 176 0.102 - 0.127: 143 Chirality restraints: 1936 Sorted by residual: chirality pdb=" CA VAL J 70 " pdb=" N VAL J 70 " pdb=" C VAL J 70 " pdb=" CB VAL J 70 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.05e-01 chirality pdb=" CA VAL R 70 " pdb=" N VAL R 70 " pdb=" C VAL R 70 " pdb=" CB VAL R 70 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA VAL Z 70 " pdb=" N VAL Z 70 " pdb=" C VAL Z 70 " pdb=" CB VAL Z 70 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 1933 not shown) Planarity restraints: 1870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR P 64 " 0.005 2.00e-02 2.50e+03 1.05e-02 1.11e+00 pdb=" C THR P 64 " -0.018 2.00e-02 2.50e+03 pdb=" O THR P 64 " 0.007 2.00e-02 2.50e+03 pdb=" N ASN P 65 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR N 64 " 0.005 2.00e-02 2.50e+03 1.05e-02 1.10e+00 pdb=" C THR N 64 " -0.018 2.00e-02 2.50e+03 pdb=" O THR N 64 " 0.007 2.00e-02 2.50e+03 pdb=" N ASN N 65 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR X 64 " 0.005 2.00e-02 2.50e+03 1.05e-02 1.10e+00 pdb=" C THR X 64 " -0.018 2.00e-02 2.50e+03 pdb=" O THR X 64 " 0.007 2.00e-02 2.50e+03 pdb=" N ASN X 65 " 0.006 2.00e-02 2.50e+03 ... (remaining 1867 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 3000 2.82 - 3.34: 8788 3.34 - 3.86: 18741 3.86 - 4.38: 21256 4.38 - 4.90: 43605 Nonbonded interactions: 95390 Sorted by model distance: nonbonded pdb=" NZ LYS F 60 " pdb=" OE1 GLU G 28 " model vdw 2.295 3.120 nonbonded pdb=" NZ LYS V 60 " pdb=" OE1 GLU W 28 " model vdw 2.295 3.120 nonbonded pdb=" OE1 GLU M 28 " pdb=" NZ LYS P 60 " model vdw 2.296 3.120 nonbonded pdb=" OE1 GLU Y 28 " pdb=" NZ LYS L 60 " model vdw 2.296 3.120 nonbonded pdb=" OE1 GLU Q 28 " pdb=" NZ LYS T 60 " model vdw 2.297 3.120 ... (remaining 95385 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 23.850 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 11033 Z= 0.412 Angle : 0.531 3.064 14905 Z= 0.312 Chirality : 0.052 0.127 1936 Planarity : 0.002 0.011 1870 Dihedral : 15.886 67.254 3751 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.10 % Allowed : 18.09 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.18), residues: 1562 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.14), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS Y 50 PHE 0.012 0.003 PHE T 94 TYR 0.009 0.002 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 245 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: F 96 LYS cc_start: 0.8253 (tttt) cc_final: 0.8034 (tttp) REVERT: G 32 LYS cc_start: 0.8452 (ttmt) cc_final: 0.8227 (mtpp) REVERT: G 35 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7519 (mm-30) REVERT: G 43 LYS cc_start: 0.8500 (mttt) cc_final: 0.8118 (mtpt) REVERT: U 21 LYS cc_start: 0.8304 (mttp) cc_final: 0.8075 (mttm) REVERT: U 43 LYS cc_start: 0.8482 (mttt) cc_final: 0.8212 (mtpt) REVERT: U 83 GLU cc_start: 0.7386 (tt0) cc_final: 0.6902 (tt0) REVERT: U 87 SER cc_start: 0.8885 (p) cc_final: 0.8537 (m) REVERT: V 97 LYS cc_start: 0.8401 (mtmt) cc_final: 0.8200 (mttt) REVERT: W 23 LYS cc_start: 0.7896 (mttt) cc_final: 0.7602 (mtpp) REVERT: W 43 LYS cc_start: 0.8420 (mttt) cc_final: 0.8196 (mtpt) REVERT: W 83 GLU cc_start: 0.7794 (tt0) cc_final: 0.7497 (tt0) REVERT: Y 23 LYS cc_start: 0.7955 (mttt) cc_final: 0.7589 (mtpp) REVERT: N 43 LYS cc_start: 0.9099 (mttp) cc_final: 0.8863 (mttp) REVERT: O 43 LYS cc_start: 0.8592 (mttt) cc_final: 0.8296 (mttm) REVERT: Q 57 GLU cc_start: 0.8095 (tt0) cc_final: 0.7871 (tt0) REVERT: S 35 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7339 (mm-30) outliers start: 12 outliers final: 3 residues processed: 256 average time/residue: 0.2838 time to fit residues: 97.2399 Evaluate side-chains 216 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 213 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain Z residue 37 VAL Chi-restraints excluded: chain P residue 37 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 8.9990 chunk 116 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 50 HIS V 50 HIS W 50 HIS X 50 HIS Y 50 HIS Y 79 GLN Z 50 HIS ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN N 50 HIS ** N 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 50 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11033 Z= 0.336 Angle : 0.483 4.509 14905 Z= 0.278 Chirality : 0.052 0.177 1936 Planarity : 0.002 0.020 1870 Dihedral : 4.895 20.723 1609 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.57 % Allowed : 15.06 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.18), residues: 1562 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.14), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS P 50 PHE 0.010 0.002 PHE H 94 TYR 0.013 0.002 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 207 time to evaluate : 1.204 Fit side-chains REVERT: E 35 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7830 (mm-30) REVERT: E 43 LYS cc_start: 0.8378 (mttt) cc_final: 0.7895 (mtpt) REVERT: G 23 LYS cc_start: 0.7798 (mtpp) cc_final: 0.7545 (ttpt) REVERT: G 35 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7468 (mm-30) REVERT: J 97 LYS cc_start: 0.8584 (mtmt) cc_final: 0.8268 (mttm) REVERT: U 43 LYS cc_start: 0.8418 (mttt) cc_final: 0.8115 (mtpt) REVERT: V 58 LYS cc_start: 0.9124 (mttt) cc_final: 0.8893 (mttp) REVERT: W 23 LYS cc_start: 0.8037 (mttt) cc_final: 0.7773 (mtmt) REVERT: Y 23 LYS cc_start: 0.8057 (mttt) cc_final: 0.7653 (mtpp) REVERT: M 23 LYS cc_start: 0.8150 (mtpp) cc_final: 0.7705 (mptt) REVERT: O 43 LYS cc_start: 0.8651 (mttt) cc_final: 0.8288 (mttm) REVERT: R 88 ILE cc_start: 0.9039 (mp) cc_final: 0.8824 (mt) REVERT: S 23 LYS cc_start: 0.7833 (mttm) cc_final: 0.7454 (mtpt) REVERT: S 32 LYS cc_start: 0.8497 (ttmt) cc_final: 0.8183 (mtpp) REVERT: S 35 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7393 (mm-30) REVERT: S 43 LYS cc_start: 0.8846 (mttt) cc_final: 0.8415 (mtpt) REVERT: T 58 LYS cc_start: 0.8685 (mttt) cc_final: 0.8432 (mttt) outliers start: 28 outliers final: 19 residues processed: 225 average time/residue: 0.2800 time to fit residues: 84.6772 Evaluate side-chains 217 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 198 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain S residue 75 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 151 optimal weight: 0.0000 chunk 124 optimal weight: 7.9990 chunk 138 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 overall best weight: 2.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 HIS ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 62 GLN L 62 GLN ** M 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 50 HIS N 62 GLN ** N 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 50 HIS P 50 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 11033 Z= 0.425 Angle : 0.510 4.782 14905 Z= 0.292 Chirality : 0.052 0.162 1936 Planarity : 0.002 0.014 1870 Dihedral : 5.039 17.602 1606 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.39 % Allowed : 16.71 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.18), residues: 1562 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.14), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS V 50 PHE 0.009 0.002 PHE H 94 TYR 0.015 0.002 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 1.152 Fit side-chains REVERT: E 35 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7825 (mm-30) REVERT: E 43 LYS cc_start: 0.8479 (mttt) cc_final: 0.8003 (mtpt) REVERT: G 35 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7537 (mm-30) REVERT: J 97 LYS cc_start: 0.8628 (mtmt) cc_final: 0.8259 (mttm) REVERT: U 43 LYS cc_start: 0.8436 (mttt) cc_final: 0.8111 (mtpt) REVERT: V 58 LYS cc_start: 0.9149 (mttt) cc_final: 0.8883 (mttt) REVERT: W 23 LYS cc_start: 0.8143 (mttt) cc_final: 0.7849 (mtmt) REVERT: Y 23 LYS cc_start: 0.8199 (mttt) cc_final: 0.7792 (mtpp) REVERT: M 23 LYS cc_start: 0.8208 (mtpp) cc_final: 0.7762 (mptt) REVERT: O 43 LYS cc_start: 0.8663 (mttt) cc_final: 0.8290 (mttm) REVERT: Q 57 GLU cc_start: 0.8616 (tt0) cc_final: 0.8393 (tt0) REVERT: R 88 ILE cc_start: 0.9072 (mp) cc_final: 0.8868 (mt) REVERT: S 35 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7551 (mm-30) REVERT: S 43 LYS cc_start: 0.8828 (mttt) cc_final: 0.8415 (mtpt) REVERT: T 97 LYS cc_start: 0.8569 (mtmt) cc_final: 0.8369 (mttt) outliers start: 26 outliers final: 23 residues processed: 217 average time/residue: 0.2761 time to fit residues: 81.1247 Evaluate side-chains 215 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain S residue 75 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 ASN V 50 HIS ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 62 GLN N 50 HIS ** N 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 50 HIS P 50 HIS P 62 GLN S 50 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 11033 Z= 0.513 Angle : 0.550 4.072 14905 Z= 0.314 Chirality : 0.053 0.158 1936 Planarity : 0.002 0.014 1870 Dihedral : 5.257 18.257 1606 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.31 % Allowed : 18.09 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.18), residues: 1562 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.14), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS F 50 PHE 0.011 0.002 PHE H 94 TYR 0.018 0.003 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 205 time to evaluate : 1.307 Fit side-chains REVERT: E 35 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8040 (mm-30) REVERT: E 43 LYS cc_start: 0.8492 (mttt) cc_final: 0.8006 (mtpt) REVERT: G 35 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7609 (mm-30) REVERT: I 58 LYS cc_start: 0.8464 (mtpt) cc_final: 0.7990 (mttt) REVERT: J 72 THR cc_start: 0.9114 (p) cc_final: 0.8652 (m) REVERT: J 96 LYS cc_start: 0.9091 (tttt) cc_final: 0.8834 (tttm) REVERT: J 97 LYS cc_start: 0.8629 (mtmt) cc_final: 0.8274 (mttm) REVERT: U 43 LYS cc_start: 0.8425 (mttt) cc_final: 0.8108 (mtpt) REVERT: V 58 LYS cc_start: 0.9172 (mttt) cc_final: 0.8910 (mttp) REVERT: W 23 LYS cc_start: 0.8204 (mttt) cc_final: 0.7901 (mtmt) REVERT: W 43 LYS cc_start: 0.8444 (mttt) cc_final: 0.8205 (mtpt) REVERT: Y 23 LYS cc_start: 0.8297 (mttt) cc_final: 0.7860 (mtpp) REVERT: Y 57 GLU cc_start: 0.8496 (tt0) cc_final: 0.8257 (tt0) REVERT: M 23 LYS cc_start: 0.8226 (mtpp) cc_final: 0.7811 (mptt) REVERT: O 43 LYS cc_start: 0.8687 (mttt) cc_final: 0.8307 (mttm) REVERT: Q 57 GLU cc_start: 0.8592 (tt0) cc_final: 0.8367 (tt0) REVERT: R 88 ILE cc_start: 0.9077 (mp) cc_final: 0.8873 (mt) REVERT: S 35 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7611 (mm-30) REVERT: S 43 LYS cc_start: 0.8855 (mttt) cc_final: 0.8425 (mtpt) REVERT: S 57 GLU cc_start: 0.8346 (tt0) cc_final: 0.8121 (tt0) outliers start: 36 outliers final: 29 residues processed: 226 average time/residue: 0.2790 time to fit residues: 84.9225 Evaluate side-chains 229 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 HIS ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 50 HIS ** N 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 50 HIS P 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 11033 Z= 0.451 Angle : 0.520 5.733 14905 Z= 0.297 Chirality : 0.052 0.131 1936 Planarity : 0.002 0.011 1870 Dihedral : 5.196 18.234 1606 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.58 % Allowed : 18.00 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.18), residues: 1562 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.14), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS F 50 PHE 0.010 0.002 PHE H 94 TYR 0.018 0.003 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 210 time to evaluate : 1.238 Fit side-chains REVERT: E 35 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8035 (mm-30) REVERT: E 43 LYS cc_start: 0.8495 (mttt) cc_final: 0.7988 (mtpt) REVERT: G 35 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7611 (mm-30) REVERT: I 58 LYS cc_start: 0.8513 (mtpt) cc_final: 0.7988 (mttp) REVERT: J 72 THR cc_start: 0.9121 (p) cc_final: 0.8665 (m) REVERT: J 96 LYS cc_start: 0.9077 (tttt) cc_final: 0.8827 (tttm) REVERT: J 97 LYS cc_start: 0.8647 (mtmt) cc_final: 0.8278 (mttm) REVERT: U 43 LYS cc_start: 0.8419 (mttt) cc_final: 0.8107 (mtpt) REVERT: V 58 LYS cc_start: 0.9167 (mttt) cc_final: 0.8898 (mttp) REVERT: W 23 LYS cc_start: 0.8212 (mttt) cc_final: 0.7911 (mtmt) REVERT: W 43 LYS cc_start: 0.8451 (mttt) cc_final: 0.8215 (mtpt) REVERT: Y 23 LYS cc_start: 0.8316 (mttt) cc_final: 0.7884 (mtpp) REVERT: Y 57 GLU cc_start: 0.8477 (tt0) cc_final: 0.8248 (tt0) REVERT: Y 58 LYS cc_start: 0.8044 (mtpt) cc_final: 0.7694 (mttt) REVERT: M 23 LYS cc_start: 0.8253 (mtpp) cc_final: 0.7851 (mptt) REVERT: O 43 LYS cc_start: 0.8669 (mttt) cc_final: 0.8292 (mttm) REVERT: S 35 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7569 (mm-30) REVERT: S 43 LYS cc_start: 0.8850 (mttt) cc_final: 0.8433 (mtpt) outliers start: 39 outliers final: 32 residues processed: 235 average time/residue: 0.2744 time to fit residues: 87.7698 Evaluate side-chains 236 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain Y residue 59 THR Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 83 GLU Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain S residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 29 optimal weight: 0.0270 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 HIS ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 GLN N 50 HIS ** N 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 50 HIS S 50 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11033 Z= 0.227 Angle : 0.427 4.192 14905 Z= 0.246 Chirality : 0.051 0.125 1936 Planarity : 0.001 0.014 1870 Dihedral : 4.811 16.574 1606 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.66 % Allowed : 19.93 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.19), residues: 1562 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.14), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS F 50 PHE 0.008 0.001 PHE H 94 TYR 0.015 0.002 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 210 time to evaluate : 1.110 Fit side-chains revert: symmetry clash REVERT: E 35 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8024 (mm-30) REVERT: E 43 LYS cc_start: 0.8410 (mttt) cc_final: 0.7945 (mtpt) REVERT: G 35 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7547 (mm-30) REVERT: I 58 LYS cc_start: 0.8516 (mtpt) cc_final: 0.8002 (mttp) REVERT: J 72 THR cc_start: 0.9147 (p) cc_final: 0.8710 (m) REVERT: J 97 LYS cc_start: 0.8636 (mtmt) cc_final: 0.8312 (mttm) REVERT: J 99 GLN cc_start: 0.7422 (mt0) cc_final: 0.7169 (mm-40) REVERT: U 43 LYS cc_start: 0.8407 (mttt) cc_final: 0.8081 (mtpt) REVERT: V 58 LYS cc_start: 0.9127 (mttt) cc_final: 0.8884 (mttt) REVERT: W 23 LYS cc_start: 0.8201 (mttt) cc_final: 0.7877 (mtmt) REVERT: Y 23 LYS cc_start: 0.8296 (mttt) cc_final: 0.7872 (mtpp) REVERT: Y 57 GLU cc_start: 0.8402 (tt0) cc_final: 0.8187 (tt0) REVERT: Y 58 LYS cc_start: 0.8024 (mtpt) cc_final: 0.7696 (mttt) REVERT: Y 75 THR cc_start: 0.8892 (OUTLIER) cc_final: 0.8691 (m) REVERT: M 23 LYS cc_start: 0.8235 (mtpp) cc_final: 0.7787 (mptt) REVERT: O 43 LYS cc_start: 0.8627 (mttt) cc_final: 0.8258 (mttm) REVERT: S 35 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7479 (mm-30) REVERT: S 43 LYS cc_start: 0.8823 (mttt) cc_final: 0.8333 (mtpt) outliers start: 29 outliers final: 18 residues processed: 229 average time/residue: 0.2696 time to fit residues: 84.0323 Evaluate side-chains 222 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 83 GLU Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 64 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 108 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 79 GLN ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 50 HIS ** N 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 50 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11033 Z= 0.356 Angle : 0.476 5.020 14905 Z= 0.272 Chirality : 0.051 0.127 1936 Planarity : 0.002 0.013 1870 Dihedral : 4.982 17.189 1606 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.31 % Allowed : 19.28 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.19), residues: 1562 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.14), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS F 50 PHE 0.009 0.002 PHE H 94 TYR 0.016 0.002 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 205 time to evaluate : 1.227 Fit side-chains revert: symmetry clash REVERT: E 35 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7838 (mm-30) REVERT: E 43 LYS cc_start: 0.8460 (mttt) cc_final: 0.7977 (mtpt) REVERT: G 35 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7554 (mm-30) REVERT: I 58 LYS cc_start: 0.8487 (mtpt) cc_final: 0.8008 (mttt) REVERT: J 72 THR cc_start: 0.9162 (p) cc_final: 0.8682 (m) REVERT: J 97 LYS cc_start: 0.8648 (mtmt) cc_final: 0.8300 (mttm) REVERT: U 43 LYS cc_start: 0.8420 (mttt) cc_final: 0.8109 (mtpt) REVERT: V 58 LYS cc_start: 0.9141 (mttt) cc_final: 0.8879 (mttp) REVERT: W 23 LYS cc_start: 0.8180 (mttt) cc_final: 0.7889 (mtmt) REVERT: W 43 LYS cc_start: 0.8450 (mttt) cc_final: 0.8225 (mtpt) REVERT: Y 23 LYS cc_start: 0.8350 (mttt) cc_final: 0.7954 (mtpp) REVERT: Y 57 GLU cc_start: 0.8454 (tt0) cc_final: 0.8239 (tt0) REVERT: Y 75 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8699 (m) REVERT: M 23 LYS cc_start: 0.8248 (mtpp) cc_final: 0.7806 (mptt) REVERT: O 43 LYS cc_start: 0.8681 (mttt) cc_final: 0.8322 (mttm) REVERT: S 35 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7504 (mm-30) REVERT: S 43 LYS cc_start: 0.8846 (mttt) cc_final: 0.8353 (mtpt) outliers start: 36 outliers final: 25 residues processed: 227 average time/residue: 0.2654 time to fit residues: 82.0842 Evaluate side-chains 227 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 201 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 83 GLU Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain S residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 HIS ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 HIS ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 50 HIS ** N 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 50 HIS P 50 HIS S 50 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11033 Z= 0.362 Angle : 0.478 5.208 14905 Z= 0.273 Chirality : 0.051 0.127 1936 Planarity : 0.002 0.013 1870 Dihedral : 5.014 17.330 1606 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.31 % Allowed : 18.92 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.19), residues: 1562 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.14), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS F 50 PHE 0.009 0.002 PHE H 94 TYR 0.016 0.002 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 1.248 Fit side-chains revert: symmetry clash REVERT: E 35 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7834 (mm-30) REVERT: E 43 LYS cc_start: 0.8508 (mttt) cc_final: 0.8036 (mtpt) REVERT: G 35 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7596 (mm-30) REVERT: I 58 LYS cc_start: 0.8482 (mtpt) cc_final: 0.7988 (mttt) REVERT: J 72 THR cc_start: 0.9139 (p) cc_final: 0.8685 (m) REVERT: J 96 LYS cc_start: 0.9022 (tttt) cc_final: 0.8749 (tttm) REVERT: J 97 LYS cc_start: 0.8633 (mtmt) cc_final: 0.8298 (mttm) REVERT: U 43 LYS cc_start: 0.8419 (mttt) cc_final: 0.8111 (mtpt) REVERT: W 23 LYS cc_start: 0.8108 (mttt) cc_final: 0.7821 (mtmt) REVERT: W 43 LYS cc_start: 0.8459 (mttt) cc_final: 0.8231 (mtpt) REVERT: Y 23 LYS cc_start: 0.8368 (mttt) cc_final: 0.8157 (mttp) REVERT: Y 57 GLU cc_start: 0.8453 (tt0) cc_final: 0.8237 (tt0) REVERT: Y 75 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8700 (m) REVERT: M 23 LYS cc_start: 0.8236 (mtpp) cc_final: 0.7823 (mptt) REVERT: O 43 LYS cc_start: 0.8692 (mttt) cc_final: 0.8330 (mttm) REVERT: S 35 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7525 (mm-30) REVERT: S 43 LYS cc_start: 0.8847 (mttt) cc_final: 0.8360 (mtpt) outliers start: 36 outliers final: 27 residues processed: 220 average time/residue: 0.2691 time to fit residues: 80.4555 Evaluate side-chains 226 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 50 HIS Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 83 GLU Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain S residue 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 42 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 137 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 HIS ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 HIS ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 50 HIS ** N 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 50 HIS P 50 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11033 Z= 0.350 Angle : 0.475 5.512 14905 Z= 0.272 Chirality : 0.051 0.128 1936 Planarity : 0.002 0.013 1870 Dihedral : 5.010 17.358 1606 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.31 % Allowed : 18.82 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.19), residues: 1562 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.14), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS F 50 PHE 0.009 0.001 PHE H 94 TYR 0.015 0.002 TYR S 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: E 35 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7989 (mm-30) REVERT: E 43 LYS cc_start: 0.8530 (mttt) cc_final: 0.8048 (mtpt) REVERT: G 35 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7594 (mm-30) REVERT: I 58 LYS cc_start: 0.8530 (mtpt) cc_final: 0.8034 (mttt) REVERT: J 72 THR cc_start: 0.9140 (p) cc_final: 0.8681 (m) REVERT: J 96 LYS cc_start: 0.9024 (tttt) cc_final: 0.8745 (tttm) REVERT: J 97 LYS cc_start: 0.8620 (mtmt) cc_final: 0.8291 (mttm) REVERT: U 43 LYS cc_start: 0.8419 (mttt) cc_final: 0.8110 (mtpt) REVERT: W 23 LYS cc_start: 0.8121 (mttt) cc_final: 0.7843 (mtmt) REVERT: W 43 LYS cc_start: 0.8452 (mttt) cc_final: 0.8230 (mtpt) REVERT: Y 57 GLU cc_start: 0.8459 (tt0) cc_final: 0.8240 (tt0) REVERT: M 23 LYS cc_start: 0.8228 (mtpp) cc_final: 0.7817 (mptt) REVERT: O 43 LYS cc_start: 0.8689 (mttt) cc_final: 0.8327 (mttm) REVERT: S 35 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7546 (mm-30) REVERT: S 43 LYS cc_start: 0.8858 (mttt) cc_final: 0.8365 (mtpt) outliers start: 36 outliers final: 29 residues processed: 222 average time/residue: 0.2707 time to fit residues: 81.4137 Evaluate side-chains 226 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 197 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 50 HIS Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain Y residue 59 THR Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 83 GLU Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain S residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 HIS ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 HIS ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 50 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 11033 Z= 0.477 Angle : 0.535 6.457 14905 Z= 0.304 Chirality : 0.052 0.127 1936 Planarity : 0.002 0.017 1870 Dihedral : 5.231 18.184 1606 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.12 % Allowed : 18.82 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.19), residues: 1562 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS F 50 PHE 0.010 0.002 PHE H 94 TYR 0.017 0.003 TYR I 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 206 time to evaluate : 1.189 Fit side-chains revert: symmetry clash REVERT: E 35 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7798 (mm-30) REVERT: E 43 LYS cc_start: 0.8524 (mttt) cc_final: 0.8035 (mtpt) REVERT: G 35 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7607 (mm-30) REVERT: I 58 LYS cc_start: 0.8500 (mtpt) cc_final: 0.7964 (mttp) REVERT: J 72 THR cc_start: 0.9142 (p) cc_final: 0.8655 (m) REVERT: J 96 LYS cc_start: 0.9054 (tttt) cc_final: 0.8788 (tttm) REVERT: J 97 LYS cc_start: 0.8624 (mtmt) cc_final: 0.8280 (mttm) REVERT: U 43 LYS cc_start: 0.8417 (mttt) cc_final: 0.8104 (mtpt) REVERT: W 43 LYS cc_start: 0.8461 (mttt) cc_final: 0.8227 (mtpt) REVERT: Y 57 GLU cc_start: 0.8514 (tt0) cc_final: 0.8301 (tt0) REVERT: M 23 LYS cc_start: 0.8204 (mtpp) cc_final: 0.7801 (mptt) REVERT: O 43 LYS cc_start: 0.8681 (mttt) cc_final: 0.8315 (mttm) REVERT: S 35 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7579 (mm-30) REVERT: S 43 LYS cc_start: 0.8872 (mttt) cc_final: 0.8379 (mtpt) outliers start: 34 outliers final: 29 residues processed: 225 average time/residue: 0.2879 time to fit residues: 88.1779 Evaluate side-chains 233 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 50 HIS Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain Y residue 59 THR Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 83 GLU Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain S residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 5.9990 chunk 37 optimal weight: 0.3980 chunk 112 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 33 optimal weight: 0.0970 chunk 122 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 125 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.0050 chunk 107 optimal weight: 3.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 HIS ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 HIS Y 79 GLN ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN N 50 HIS ** N 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 50 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.093253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.074479 restraints weight = 14032.701| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.42 r_work: 0.3016 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11033 Z= 0.165 Angle : 0.410 6.418 14905 Z= 0.236 Chirality : 0.051 0.123 1936 Planarity : 0.001 0.013 1870 Dihedral : 4.702 16.803 1606 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.02 % Allowed : 20.11 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.19), residues: 1562 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS F 50 PHE 0.006 0.001 PHE H 94 TYR 0.013 0.002 TYR I 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2609.90 seconds wall clock time: 48 minutes 27.83 seconds (2907.83 seconds total)